Microbiology spectrum最新文献

{"title":"Identification and characterization of <i>ethR</i> and <i>ethA</i> genes impacting the sensitivity of <i>Mycobacterium abscessus</i> to ethionamide.","authors":"Xiaofan Zhang, Lijie Li, Ziwen Lu, Chaohui Duan, H M Adnan Hameed, Aweke Mulu Belachew, Cuiting Fang, Xirong Tian, Xinyue Wang, Hongyi Chen, Liqiang Feng, Matthew B McNeil, Dongxin Liu, Shuai Wang, Tianyu Zhang","doi":"10.1128/spectrum.00638-26","DOIUrl":"10.1128/spectrum.00638-26","url":null,"abstract":"<p><p><i>Mycobacterium abscessus</i> is a rapidly growing non-tuberculous mycobacterium with rising global incidence. This pathogen exhibits intrinsic resistance to most antibiotics, presenting a major public health threat. Ethionamide (ETH) requires bioactivation by monooxygenase EthA to form the active ETH-NAD adduct. We previously identified MAB_3513 (NudC) as a phosphohydrolase that confers intrinsic resistance to <i>M. abscessus</i> by hydrolyzing this adduct. However, deletion of <i>nudC</i> results in only partial susceptibility to ETH, indicating the existence of additional resistance mechanisms. This study identified MAB_0984 as the EthR regulator in <i>M. abscessus</i>. Deletion of <i>ethR</i> in a <i>nudC</i> knockout background (ΔΔ<i>ethR</i>) significantly enhanced ETH-NAD adduct accumulation, leading to hypersusceptibility to ETH. Notably, the Δ<i>ethR</i> mutant exhibited higher susceptibility than Δ<i>nudC</i>, demonstrating that EthR is a more dominant mediator of ETH resistance than NudC. Furthermore, MAB_0985 (EthA1) and MAB_0103 (EthA2) are the principal ETH-activating monooxygenases in <i>M. abscessus</i>. Deletion of either gene alone or in combination in the Δ<i>nudC</i> reduced adduct formation and increased resistance, while the triple mutant ΔΔ<i>ethA1</i>Δ<i>ethA2</i> restored wild-type resistance. Using an intergenic region-enhanced green fluorescent protein reporter system and quantitative reverse transcription-PCR, we demonstrated that EthR confers resistance by specifically suppressing <i>ethA1</i> expression in <i>M. abscessus</i>. The <i>Mycobacterium tuberculosis</i> EthR inhibitor BDM31343 could boost the efficacy of ETH against <i>M. abscessus</i> by inhibiting EthR. Collectively, this study identified the <i>ethR</i> and <i>ethA</i> genes in <i>M. abscessus</i> for the first time and elucidated their role in mediating resistance to ETH. Therefore, EthR is a promising target for potentiating the efficacy of ETH against <i>M. abscessus</i>.IMPORTANCE<i>Mycobacterium abscessus</i> constitutes an escalating global health threat, primarily due to its intrinsic resistance to most antibiotics. This study identifies MAB_0984 (EthR) as a dominant resistance determinant that exerts a more profound impact on ethionamide (ETH) susceptibility than the previously characterized NudC. We demonstrate that EthR mediates resistance by specifically repressing the expression of EthA1 (MAB_0985), one of the primary monooxygenases responsible for ETH bioactivation. The <i>Mycobacterium tuberculosis</i> EthR inhibitor BDM31343 potentiated the activity of ETH against <i>M. abscessus</i> through inhibition of EthR. These findings elucidate the mechanism of ETH resistance in <i>M. abscessus</i>, identifying EthR as a promising target for boosting the efficacy of ETH against <i>M. abscessus</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0063826"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibiotic-induced cellular enlargement drives phage synergy and resensitizes carbapenem-resistant <i>Acinetobacter baumannii</i>.","authors":"Arrita Rueangrit, Wanna Sudhikaran, Arom Sombutmark, Pisamai Pinsrithong, Lalitwadee Chotuk, Ampapan Naknaen","doi":"10.1128/spectrum.01424-26","DOIUrl":"10.1128/spectrum.01424-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Carbapenem-resistant &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; (CRAB) represents a critical clinical challenge, as phage monotherapy is frequently compromised by the rapid emergence of bacterial resistance. This study characterizes phiAR008, a newly isolated &lt;i&gt;Hadassahvirus&lt;/i&gt; phage with therapeutic potential against clinical CRAB isolates, and evaluates its synergistic efficacy alongside five antibiotic classes to develop robust combination therapies. Although phiAR008 monotherapy initially reduced bacterial growth, rapid bacterial regrowth occurred. In contrast, combination treatment with subinhibitory concentrations of meropenem (MEM) or ciprofloxacin (CIP) produced complete bacterial clearance &lt;i&gt;in vitro&lt;/i&gt; and significantly enhanced antibacterial activity compared with either treatment alone. MEM and CIP induced distinct morphological changes, including spheroid enlargement and filamentation, respectively, resulting in increased bacterial cell surface area. These morphological alterations were associated with accelerated phage adsorption and increased intracellular phage accumulation during the early stages of infection, whereas the final phage yield remained unchanged, suggesting that antibiotic-induced cell enlargement primarily enhances early infection kinetics rather than phage productivity. In contrast, antibiotics that did not substantially alter bacterial morphology, including colistin, rifampin, and chloramphenicol, exhibited limited synergy with phiAR008. In a &lt;i&gt;Galleria mellonella&lt;/i&gt; infection model, phiAR008-MEM and phiAR008-CIP combination therapy significantly improved larval survival compared with phage or antibiotic monotherapy. Phage-resistant isolates recovered following combination treatment also exhibited reduced virulence and altered antibiotic susceptibility. Although the genetic and mechanistic basis of these phenotypic changes remains to be determined, our findings indicate that antibiotic-induced bacterial morphological changes may contribute to phage-antibiotic synergy by enhancing early phage-host interactions. These results support the rational optimization of phage-antibiotic combinations as a promising therapeutic strategy for refractory CRAB infections.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Phage-antibiotic synergy offers a promising strategy to overcome the therapeutic limitations of phage monotherapy against CRAB. In this study, phiAR008 showed limited standalone killing because bacterial regrowth and phage resistance emerged rapidly. However, when combined with specific antibiotics, especially meropenem and ciprofloxacin, phiAR008 produced strong synergistic antibacterial activity, leading to rapid and complete bacterial eradication &lt;i&gt;in vitro&lt;/i&gt; and improved survival &lt;i&gt;in vivo&lt;/i&gt;. Importantly, synergy was not universal across antibiotic classes, indicating that the choice of partner drug is critical. Our findings further show that synergy is mechanistically linked to antibiotic-induced changes in bacterial","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0142426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two cysteine dioxygenase homologs contribute to the fitness and virulence of a human pathogen.","authors":"Argha Saha, Denisa Petráčková, Jana Holubová, Martin Beles, Ivana Čurnová, Ondřej Staněk, Branislav Večerek","doi":"10.1128/spectrum.01414-26","DOIUrl":"10.1128/spectrum.01414-26","url":null,"abstract":"<p><p><i>Bordetella pertussis</i> is a strictly human, re-emerging respiratory pathogen and the causative agent of whooping cough. Through its adaptation to humans, <i>B. pertussis</i> decayed or lost genes of the sulfate assimilation pathway and, consequently, must obtain cysteine from the host. Previously, we showed that the sulfur metabolism of <i>B. pertussis</i> is substantially rewired during infection of human macrophages. Here, we investigated the role of several cysteine metabolism- and transport-related genes in the fitness and virulence of this pathogen. We show that excess cysteine strongly induces the expression of genes encoding two cysteine dioxygenase (CDO) homologs, BP2871 and BP3011, and a putative sulfite exporter, BP2808. The mutant lacking both cysteine dioxygenase genes exhibits impaired growth and severely reduced secretion of pertussis toxin under excess cysteine conditions <i>in vitro</i> and attenuated virulence <i>in vivo</i>. Intriguingly, both cysteine dioxygenases contain a cysteine residue near the active site, a feature typical of mammalian enzymes and associated with increased activity and stability of CDOs. Notably, replacing this cysteine with glycine in both CDOs led to impaired growth of the mutant and slightly reduced secretion of pertussis toxin and cytotoxicity. We also demonstrate the essential role of the sulfite exporter BP2808 and γ-glutamyl-cysteine synthase BP0598 in the adaptation of <i>B. pertussis</i> to cysteine-induced stress. Overall, our data suggest that sulfur metabolism has been effectively streamlined in <i>B. pertussis</i> and plays an important role at the host-pathogen interface.IMPORTANCESulfur is one of the essential nutrients required by cells for growth, and cysteine is central to sulfur metabolism. While most bacteria prefer environmentally available sulfate as their cysteine source, several bacterial pathogens rely on cysteine provided by the host. Here, we show that <i>Bordetella pertussis</i>, the causative agent of whooping cough, has simplified its sulfur metabolism. Our data suggest that two cysteine dioxygenase homologs and sulfite exporter play key roles in sulfur homeostasis and redox balance. Both dioxygenases enable the pathogen to use cysteine as a source of sulfur, and the sulfite exporter removes the toxic byproduct of cysteine conversion. Importantly, the lack of cysteine dioxygenase activity leads to aberrant secretion of pertussis toxin, one of the essential virulence factors, resulting in attenuated virulence of the pathogen. We suggest that cysteine auxotrophy can be considered part of an infection strategy that assists <i>B. pertussis</i> in adaptation to its human host.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0141426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The establishment of a universal blocking ELISA for echinococcosis using immunoglobulin against a new conserved linear B-cell epitope.","authors":"Guoyan Zhou, Lijuan Zheng, Zhendong Xin, Jun He, Zhi Li, Hong Duo, Ru Meng, Zhihong Guo, Yong Fu","doi":"10.1128/spectrum.03933-25","DOIUrl":"10.1128/spectrum.03933-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Echinococcosis is a neglected tropical disease that poses a severe threat to global public health and socioeconomic development. Given its alarming global spread, there is an urgent need to develop accurate diagnostic methods to support targeted and personalized treatment. &lt;i&gt;Echinococcus multilocularis&lt;/i&gt; Em18 has been demonstrated to exhibit the most prominent diagnostic relevance in the progression of alveolar echinococcosis (AE). In this study, six highly specific monoclonal antibodies (mAbs) against the Em18 protein-designated 8G6F, 11E2E, 11E7C, 11E7E, 11E8C, and 11E10D-were generated using hybridoma technology. Indirect ELISA showed that the supernatant titers ranged from 1:1,600 to 1:12,800, while the ascites titers varied from 1:128,000 to 1:512,000. Further analysis indicated that all mAbs belonged to the IgG1 κ isotype. After purification, the ascites-derived mAbs exhibited expected heavy-chain and light-chain bands at approximately 50 kDa and 25 kDa, respectively. Notably, western blot and indirect immunofluorescence assay collectively demonstrated that all mAbs exhibited high specificity for recombinant Em18 protein of approximately 18.65 kDa. Through peptide scanning technology, we identified the antigenic epitope recognized by six mAbs as the region &lt;sup&gt;99&lt;/sup&gt;RMREKHDAKHKS&lt;sup&gt;108&lt;/sup&gt;, a highly conserved linear B-cell epitope on the Em18 protein. Amino acid sequence alignment confirmed the complete conservation of this epitope, which is surface-exposed. Furthermore, the optimal blocking antibody 11E8C was selected and labeled with horseradish peroxidase (HRP) based on which a blocking ELISA was established using the anti-Em18 mAbs. Serum samples with a percent inhibition (PI) ≥22.48% were determined as positive, and those with PI ≤17.64% as negative. This method showed no cross-reactivity with positive sera against &lt;i&gt;Toxoplasma gondii&lt;/i&gt;, &lt;i&gt;Babesia&lt;/i&gt; spp., &lt;i&gt;Cysticercus tenuicollis&lt;/i&gt;, &lt;i&gt;Coenurus cerebralis&lt;/i&gt;, and other non-echinococcosis pathogens. Sensitivity testing showed a positive detection rate of 90%, and positive signals remained stable even when positive sera were diluted up to 1:16. The intra-assay and inter-assay coefficients of variation (CV) were both below 10%. In a concordance evaluation using 47 clinical serum samples from cattle and sheep, the overall agreement between our assay and a commercial kit was 93.62%. Furthermore, the mAbs developed in this study accurately identified intermediate and advanced AE infections, providing a reliable tool for assessing disease progression. Importantly, its cross-reactivity with cystic echinococcosis (CE)-infected sera demonstrates promising potential for the broad-spectrum serodiagnosis of echinococcosis. Collectively, these results suggest that this study provides a novel technical resource for improving serological detection and developing early diagnostic reagents for echinococcosis and offers experimental support for the surveillance, prevention, cont","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0393325"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Repurposing Penfluridol to combat mycobacteria via bioenergetic collapse.","authors":"Yunbing Li, Xiaofan Li, Guangfen Zhang, Chunli Li, Changting Yin, Yuanyuan Li, Jiani Jiang, Yi Yang, Zhiqiang Yang, Yinli Liu, Xiangkun Zeng, Jiayi You, Yi Liu, Ahui Li, Chang Jiang, Chen Xu, Ning Dong","doi":"10.1128/spectrum.01919-26","DOIUrl":"10.1128/spectrum.01919-26","url":null,"abstract":"<p><p>Drug-resistant <i>Mycobacterium tuberculosis</i> (Mtb) infections constitute a persistent and severe public health crisis worldwide. Standard anti-tuberculosis (anti-TB) therapies often fail to eradicate resistant strains, resulting in poor clinical outcomes and underscoring the demand for new treatment options. Drug repurposing offers a practical and time-efficient approach to accelerate the development of new anti-mycobacterial regimens. In this work, we evaluated the antimycobacterial potency of penfluridol (PL), a Food and Drug Administration (FDA)-approved antipsychotic drug, and explored its functional mechanism against mycobacteria. Our experimental data revealed that PL compromises mycobacterial membrane integrity and depletes the proton motive force (PMF), leading to disrupted energy metabolism and mycobacterial growth inhibition. PMF depletion disables energy-reliant efflux systems, facilitates intracellular PL accumulation, and further deteriorates membrane damage, creating a sustained bactericidal effect. Notably, continuous PL exposure rarely induces stable drug resistance. These observations suggest that PL can be repurposed for treating drug-resistant TB and confirm that targeting bacterial bioenergetics is an effective strategy to overcome clinical antimicrobial resistance.</p><p><strong>Importance: </strong>Tuberculosis (TB) remains a major threat to global public health, and the widespread emergence of drug-resistant strains has substantially compromised the efficacy of existing anti-TB regimens. The scarcity of approved anti-TB drugs, combined with lengthy treatment regimens and frequent therapeutic failure, further exacerbates the global TB crisis, highlighting an urgent need for safe and effective alternative therapies. Drug repurposing serves as a time-saving and reliable strategy to accelerate anti-TB drug development. This study explores the antimycobacterial efficacy and unique working mechanism of the clinically approved agent penfluridol (PL). Our findings identify a feasible candidate for treating drug-resistant TB and provide a valuable bioenergetic-targeting strategy to combat bacterial antimicrobial resistance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0191926"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An integrated strategy of multiplex qPCR and <i>BclA</i> gene length polymorphism analysis for differentiating <i>Bacillus anthracis</i> wild-type and vaccine strains.","authors":"Jiaqi Yang, Yan Liang, Bing Liang, Yanfang Li, Lingwei Zhu, Yonggang Qu","doi":"10.1128/spectrum.00192-26","DOIUrl":"10.1128/spectrum.00192-26","url":null,"abstract":"<p><p>A combined molecular strategy was developed to accurately differentiate wild-type and vaccine strains of <i>Bacillus anthracis</i>. This approach integrates a multiplex TaqMan qPCR assay targeting the <i>BclA</i>, <i>sap</i>, and <i>cap</i> genes with conventional PCR analysis of <i>BclA</i> fragment length polymorphism. The qPCR assay demonstrated high specificity, with no cross-reactivity against other common pathogens, and exhibited a consistent limit of detection of 2.11 × 10¹ copies/μL (Cq < 35) for all three targets. Excellent repeatability was confirmed, with intra- and inter-assay coefficients of variation below 1.96% and 3.06%, respectively. Validation using 19 wild-type strains revealed two distinct qPCR profiles, and all wild-type strains were conclusively differentiated from the capsule-producing Chinese vaccine strain II and the acapsular Sterne strain by their characteristic <i>BclA</i> amplicon sizes. Through simulation PCR validation of common global canSNP genotyping (groups A, B, and C), it is possible to distinguish between wild-type and vaccine strains in China. This integrated \"multiplex qPCR-BclA length analysis\" protocol provides a reliable, sensitive, and specific tool for the precise detection and differentiation of <i>B. anthracis</i> strains in China.IMPORTANCEAnthrax, which is caused by the bacterium <i>B. anthracis</i>, remains a serious zoonotic disease. Its effective surveillance relies on precise strain identification. Currently, it is challenging to rapidly and accurately distinguish wild-type strains from vaccine strains, which hinders outbreak investigation and response. This study develops a novel molecular strategy combining multiple genetic targets to solve this critical diagnostic problem. The new method provides a reliable tool for strain differentiation, directly supporting accurate source tracing and informed decision-making during anthrax outbreaks. By improving diagnostic precision, this work contributes to strengthening public and veterinary health defenses against this persistent threat.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0019226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148865727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolite and lipid profiling of human vitreous reveals purine metabolic dysregulation and inflammatory lipid remodeling as the drivers of bacterial endophthalmitis.","authors":"Dhanwini Rudraprasad, Agimanailiu Khapuinamai, Sreyasi Maiti, Satyashree Gagan, Joveeta Joseph","doi":"10.1128/spectrum.00788-26","DOIUrl":"10.1128/spectrum.00788-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Bacterial endophthalmitis, an intraocular infection and inflammation, often progresses rapidly and leads to irreversible vision loss, especially in culture-negative cases where the diagnosis is delayed. We profiled infection-associated metabolomic and lipidomic alterations in the vitreous of patients with microbiological and clinically confirmed bacterial endophthalmitis to understand pathogenesis and identify distinct markers that drive infection and retinal injury. Untargeted metabolomic and lipidomic profiling of vitreous samples from affected patients and non-infectious retinal controls was performed using liquid chromatography coupled to tandem mass spectrometry. Metabolites and lipids with &lt;i&gt;P&lt;/i&gt;-value &lt; 0.05 were considered for further pathway-specific analysis. Metabolomic profiling distinctly segregated infected from control samples, revealing dysregulation in purine metabolism, amino acid turnover, polyamine synthesis, redox regulation, and vitamin pathways. Key metabolites, xanthine, hypoxanthine, spermine, seryl-valine, seryl-isoleucine, thymine, O-methyltyramine, and phenyltrimethylammonium, were significantly elevated. These elevations were accompanied by enhanced nucleotide degradation and increased proteolytic activity. Markers of immune activation and oxidative stress were concurrently upregulated, reflecting the broader biochemical disruption characteristic of bacterial endophthalmitis. Antioxidant seleno-L-methionine was downregulated, indicating redox imbalance. Purine, glutathione, vitamin B6, beta-alanine, and arginine-proline metabolism were broadly disrupted. Complementary lipidomics showed extensive vitreous remodeling. Alongside, fatty acids, bile acid derivatives, and membrane lipids were also dysregulated. Bacterial endophthalmitis triggers strong and consistent changes in metabolite and lipid profiles within vitreous, which reflect alterations in immune activation, oxidative stress, tissue breakdown, and metabolic reprogramming. The persistence of these biomolecular signatures in the vitreous highlights host response to infection and subsequent mechanistic elucidation of the specific drivers of retinal inflammation and progressive tissue damage.IMPORTANCEThe study highlights that bacterial endophthalmitis is not only driven by microbial burden but also by host metabolic and lipidomic reprogramming, transforming the understanding of disease pathogenesis. This study reveals metabolite-lipid networks in ocular infections, laying a critical foundation for precision medicine strategies in endophthalmitis management. Specifically, we found significant increases in key metabolites including xanthine, hypoxanthine, spermine, seryl-valine, seryl-isoleucine, thymine, O-methyltyramine, and phenyltrimethylammonium, together reflecting increased nucleotide degradation, proteolytic activity, and immune metabolic reprogramming. These molecular signatures not only provide deeper mechanistic insights into ocular infection but ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0078826"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-resolved analysis reveals disruption of gut microbial vitamin B and K₂ biosynthesis during <i>Toxoplasma gondii</i> infection in mice.","authors":"Hai-Long Yu, Hany M Elsheikha, Hai-Ping Wang, Ying-Qian Gao, Rui Liu, He Ma, Jing Jiang, Ying Li, Xiao-Xuan Zhang","doi":"10.1128/spectrum.01564-26","DOIUrl":"10.1128/spectrum.01564-26","url":null,"abstract":"<p><p><i>Toxoplasma gondii</i> infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K₂ biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across <i>de novo</i> pathways for eight B vitamins, thiamine (B₁), riboflavin (B₂), niacin (B₃), pantothenate (B₅), pyridoxine (B₆), biotin (B₇), folate (B₉), cobalamin (B₁₂), and vitamin K₂. Among the high-quality genomes, 1,665 encoded complete <i>de novo</i> pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; <i>n</i> = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (<i>nadB</i>, <i>nadA</i>, <i>nadC</i>) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD⁺ precursor production under infection-induced metabolic stress. These results suggest that <i>T. gondii</i> infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD⁺ metabolism.</p><p><strong>Importance: </strong>Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that <i>Toxoplasma gondii</i> infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD⁺ precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD⁺-related metabolism may contribute to host redox adaptation during <i>T. gondii</i> infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0156426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148906733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PMAxx dye-assisted colorimetric dual DNAzyme-LAMP (PD-cDDLAMP) for rapid phenotypic antimicrobial susceptibility testing of <i>Escherichia coli</i>.","authors":"Alaa H Sewid, Joseph H Ramos, Benti D Gelalcha, Yuri Matsuoka, Oudessa Kerro Dego, Shigetoshi Eda","doi":"10.1128/spectrum.01212-26","DOIUrl":"10.1128/spectrum.01212-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Rapid antimicrobial susceptibility testing (AST) is crucial for combating antimicrobial resistance and guiding effective therapy. Conventional phenotypic AST methods are often time-consuming, requiring 18-72 h for results, while genotypic approaches often depend on pre-existing knowledge of resistance markers. Although nucleic acid-based phenotypic AST methods have reduced turnaround time, attempts to shorten antibiotic exposure often produce only small differences between susceptible and resistant bacteria. Consequently, most loop-mediated isothermal amplification (LAMP)-based phenotypic AST assays still require prolonged antibiotic exposure (up to 4 h) or rely on sophisticated high-resolution nucleic acid detection, such as digital LAMP, to accurately detect these subtle changes, limiting their simplicity. Therefore, there is a critical need to develop a rapid assay with both short antibiotic exposure times and a simple readout. To address this unmet need, we developed PMAxx dye-assisted colorimetric Dual DNAzyme-LAMP (PD-cDDLAMP), a rapid nucleic acid-based phenotypic AST method that enhances suppression of nucleic acid amplification from antibiotic-susceptible bacteria through the selective binding of photoreactive DNA-crosslinker dye (PMAxx) to the DNA of membrane-compromised cells. This strategy enables reliable discrimination between antibiotic-resistant bacteria (\"signal-on\") and antibiotic-susceptible bacteria (\"signal-off\") after only 30 min of antibiotic exposure using a user-friendly colorimetric DNAzyme-LAMP readout system. PD-cDDLAMP achieved 91.7% sensitivity, 83.3% specificity, and 87.5% accuracy in detecting &lt;i&gt;Escherichia coli&lt;/i&gt; exposed to ampicillin and tetracycline, outperforming current methods by reducing antibiotic exposure time to just 30 min. The method was further validated in spiked milk samples, demonstrating its potential for on-site AST in dairy farming. PD-cDDLAMP's simplicity, speed, and reduced workflow complexity make it a promising tool for rapid AST.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Rapid, reliable antimicrobial susceptibility testing (AST) is essential for guiding targeted therapy and combating the escalating threat of antimicrobial resistance (AMR). However, current phenotypic ASTs are too slow for urgent decision-making, and genotypic assays cannot fully capture emerging or unknown resistance mechanisms. The PMAxx dye-assisted colorimetric dual DNAzyme-loop-mediated isothermal amplification (PD-cDDLAMP) assay introduced in this work provides a rapid nucleic acid-based phenotypic AST capable of distinguishing antibiotic-resistant from susceptible bacteria within 30 min of antibiotic exposure. By combining PMAxx-mediated suppression of nucleic acid amplification in susceptible cells with equipment-free colorimetric DNAzyme-LAMP readout, PD-cDDLAMP bridges the gap between speed and phenotypic accuracy. Its high diagnostic performance, compatibility with complex matrices such as milk, and minimal instr","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0121226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid ESBL-Carba Combo PN test for simultaneous detection of ESBL and carbapenemase activity in Enterobacterales.","authors":"Soraya Herrera-Espejo, Jacqueline Findlay, Maxime Bouvier, Clément Viguier, Maurice Klahre, Nicolas Bodart, Patrice Nordmann","doi":"10.1128/spectrum.01123-26","DOIUrl":"10.1128/spectrum.01123-26","url":null,"abstract":"<p><p>A chromogenic biochemical assay (ESBL-Carba Combo PN test) was developed for the simultaneous detection of extended-spectrum β-lactamase (ESBL) and carbapenemase activity in Enterobacterales, as well as for discrimination of clinically relevant carbapenemase classes. The assay is based on a novel chromogenic substrate, B-Lac, and a low-cost Tris-based lysis buffer, providing a unified workflow for the detection of ESBLs and carbapenemases. The test was evaluated using cultures of well-characterized clinical isolates with resistance mechanisms previously defined by whole-genome sequencing. Results were obtained after a mean preparation time of approximately 3 min per isolate and were read after 20 min and 1 h of incubation. For ESBL detection (<i>n</i> = 67), sensitivity was 93.8% and 97.8% after 20 min and 1 h of incubation, respectively, with a specificity of 100%. Carbapenemase activity (<i>n</i> = 92) was detected with 100% sensitivity and specificity at both time points. Using the combined assay (<i>n</i> = 85), ESBL and/or carbapenemase activity was detected with 100% sensitivity and specificity. For Ambler classes A and B, 100% sensitivity and specificity were reached after 20 min of incubation. Regarding class D carbapenemases, 91.3% and 95.5% sensitivity after 20 min and 1 h of incubation, respectively, were observed, with 100% specificity at both times. The ESBL-Carba Combo PN test provides a simple, low-cost (<1 USD/sample), and functional method for the simultaneous detection of the major β-lactam resistance mechanisms in Enterobacterales and for carbapenemase class discrimination within one workflow, potentially supporting earlier optimization of antimicrobial therapy and antimicrobial stewardship in routine clinical microbiology laboratories.</p><p><strong>Importance: </strong>Rapid identification of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE) is essential to optimize antimicrobial therapy and implement timely infection control measures. Most currently available rapid phenotypic assays detect these resistance mechanisms separately, increasing hands-on time, workload, reagent consumption, and cost, particularly in isolates co-producing multiple β-lactamases. In addition, discrimination between carbapenemase classes, particularly class A and class D carbapenemases, remains challenging for most biochemical assays. This study describes a simple chromogenic assay that allows the simultaneous functional detection of both enzyme types using a single substrate and a low-cost lysis buffer. By incorporating relebactam as a selective class A inhibitor, the assay improves phenotypic discrimination between class A and class D carbapenemases while preserving reliable ESBL detection. The rapid ESBL-Carba Combo PN test provides 1 h of phenotypic information on the most clinically relevant β-lactam resistance mechanisms and represents a useful tool to guide early antibiotic treatment.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0112326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}